He has extended his studies on carbohydrate binding modules to explore how glycosidehydrolases are able to select specific substrates and modes of action. Using structure-based strategies, he has exploited this fundamental understanding of enzyme specificity to engineer novel catalytic functions into these biological catalysts.

As of 2016[update], Gilbert has been dissecting the mechanisms of glycans utilisation by gut bacteria, in the human microbiota.[8] His work has led to the presentation of a selfish model for the metabolism of highly complex carbohydrates by members of this ecosystem.[9][10] His work has implications on resource allocation within the human microbiota, which could impact on dietary strategies that maximise the impact of this microbial ecology on health.